Cis-regulatory elements (CREs) play a critical role in the regulation of gene expression by mediating the interaction between transcription factors (TFs) and their target genes. Mutations within CREs can disrupt key TF binding sites, thereby altering gene expression, and thus contributing to disease. The vast majority of SNPs identified in genome-wide association studies (GWAS) of complex disease fall within non-coding regions, and is thought to affect the activity of CREs. Thus, a better understanding of the location and function of CREs is essential for interpreting the functional significance of genetic variation within non-coding regions. ENCODE and other consortium-based projects have begun to map the location of CREs in multiple cell lines and whole organs. However, our understanding of cis-regulatory architecture at the level of individual primary cell types is limited. In this proposal,we will utilize a newly developed epigenomic mapping technology, ATAC-seq, to comprehensively identify the CREs of all seven major cell classes in the mouse retina: rods, cones, horizontal cells, bipolar cells, Mller glia, amacrine cells, and ganglion cells. ATAC-seq utilizes a transposase-based approach to tag regions of open chromatin and can be applied to very small numbers of cells purified by fluorescence-activated cell sorting (FACS). This transformative approach will permit us to probe the complex interrelations between chromatin accessibility, nucleosome positioning, and TF binding on a genome-wide scale in all mouse retinal cell classes. Furthermore, we will leverage these data to probe the function of thousands of CREs within specific retinal cell types, using CRE-seq, a novel technique for high-throughput cis-regulatory analysis. Taken together, these studies will generate a comprehensive, functional map of retinal CREs that will serve as a blueprint for understanding the transcriptional networks of the retina and the effects of non-coding variants on disease. In addition, these studies will se the stage for future work that will utilize epigenomic profiling to characterize changes that occur during the process of retinal development and in the course of degeneration.